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Nat Biotechnol. 2004 Nov;22(11):1467-73.

Promoter prediction analysis on the whole human genome.

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  • 1Institute for Infocomm Research, 21 Heng Mui Keng Terrace, 119613 Singapore. bajicv@i2r.a-star.edu.sg


Promoter prediction programs (PPPs) are important for in silico gene discovery without support from expressed sequence tag (EST)/cDNA/mRNA sequences, in the analysis of gene regulation and in genome annotation. Contrary to previous expectations, a comprehensive analysis of PPPs reveals that no program simultaneously achieves sensitivity and a positive predictive value >65%. PPP performances deduced from a limited number of chromosomes or smaller data sets do not hold when evaluated at the level of the whole genome, with serious inaccuracy of predictions for non-CpG-island-related promoters. Some PPPs even perform worse than, or close to, pure random guessing.

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